OpenRaiser/Intern-Atlas huggingface dataset:
Test-Time Tuned Language Models Enable End-to-end De Novo Molecular Structure Generation from MS/MS Spectra
Venue: arXiv cs.AI 2026
Year: 2026

Tandem Mass Spectrometry is a cornerstone technique for identifying unknown small molecules in fields such as metabolomics, natural product discovery and environmental analysis. However, certain aspects, such as the probabilistic fragmentation process and size of the chemical space, make structure elucidation from such spectra highly challenging, particularly when there is a shift between the deployment and training conditions. Current methods rely on database matching of previously observed spectra of known molecules and multi-step pipelines that require intermediate fingerprint prediction or expensive fragment annotations. We introduce a novel end-to-end framework based on a transformer model that directly generates molecular structures from an input tandem mass spectrum and its corresponding molecular formula, thereby eliminating the need for manual annotations and intermediate steps, while leveraging transfer learning from simulated data. To further address the challenge of out-of-distribution spectra, we introduce a test-time tuning strategy that dynamically adapts the pre-trained model to novel experimental data. Our approach achieves a Top-1 accuracy of 3.16% on the MassSpecGym benchmark and 12.88% on the NPLIB1 datasets, considerably outperforming conventional fine-tuning. Baseline approaches are also surpassed by 27% and 67% respectively. Even when the exact reference structure is not recovered, the generated candidates are chemically informative, exhibiting high structural plausibility as reflected by strong Tanimoto similarity to the ground truth. Notably, we observe a relative improvement in average Tanimoto similarity of 83% on NPLIB1 and 64% on MassSpecGym compared to state-of-the-art methods. Our framework combines simplicity with adaptability, generating accurate molecular candidates that offer valuable guidance for expert interpretation of unseen spectra.
Beyond Understanding: Evaluating the Pragmatic Gap in LLMs' Cultural Processing of Figurative Language
Venue: arXiv cs.CL 2026
Year: 2026

We present a comprehensive evaluation of the ability of large language models (LLMs) to process culturally grounded language, specifically to understand and pragmatically use figurative expressions that encode local knowledge and cultural nuance. Using figurative language as a proxy for cultural nuance and local knowledge, we design evaluation tasks for contextual understanding, pragmatic use, and connotation interpretation in Arabic and English. We evaluate 22 open- and closed-source LLMs on Egyptian Arabic idioms, multidialectal Arabic proverbs, and English proverbs. Our results show a consistent hierarchy: the average accuracy for Arabic proverbs is 4.29% lower than for English proverbs, and performance for Egyptian idioms is 10.28% lower than for Arabic proverbs. For the pragmatic use task, accuracy drops by 14.07% relative to understanding, though providing contextual idiomatic sentences improves accuracy by 10.66%. Models also struggle with connotative meaning, reaching at most 85.58% agreement with human annotators on idioms with 100% inter-annotator agreement. These findings demonstrate that figurative language serves as an effective diagnostic for cultural reasoning: while LLMs can often interpret figurative meaning, they face challenges in using it appropriately. To support future research, we release Kinayat, the first dataset of Egyptian Arabic idioms designed for both figurative understanding and pragmatic use evaluation.
GIFT: Group-relative Implicit Fine Tuning Integrates GRPO with DPO and UNA
Venue: arXiv cs.LG 2026
Year: 2026

I propose \textbf{G}roup-relative \textbf{I}mplicit \textbf{F}ine \textbf{T}uning (GIFT), a novel reinforcement learning framework for aligning LLMs. Instead of directly maximizing cumulative rewards like PPO or GRPO, GIFT minimizes the discrepancy between implicit and explicit reward models. It combines three key ideas: (1) the online multi-response generation and normalization of GRPO, (2) the implicit reward formulation of DPO, and (3) the implicit-explicit reward alignment principle of UNA. By jointly normalizing the implicit and explicit rewards, GIFT eliminates an otherwise intractable term that prevents effective use of implicit rewards. This normalization transforms the complex reward maximization objective into a simple mean squared error (MSE) loss between the normalized reward functions, converting a non-convex optimization problem into a convex, stable, and analytically differentiable formulation. Unlike offline methods such as DPO and UNA, GIFT remains on-policy and thus retains exploration capability. Compared to GRPO, it requires fewer hyperparameters, converges faster, and generalizes better with significantly reduced training overfitting. Empirically, GIFT achieves superior reasoning and alignment performance on mathematical benchmarks while remaining computationally efficient.
Importance of Overlapping Network Nodes in Influence Spreading
Venue: arXiv cs.SI 2026
Year: 2026

In complex networks there are overlapping substructures or "circles" that consist of nodes belonging to multiple cohesive subgroups. Yet the role of these overlapping nodes in influence spreading processes remains underexplored. In the present study, we analyse networks with circle structures using a probabilistic influence spreading model for processes of simple and complex contagion. We quantify the roles of nodes using three metrics, i.e., In-Centrality, Out-Centrality, and Betweenness Centrality that represent the susceptibility, spreading power, and mediatory role of nodes, respectively, and find that at each stage of the spreading process the overlapping nodes consistently exhibit greater influence than the non-overlapping ones. Furthermore, we observe that the criteria to define circles shape the overlapping effects. When we restrict our analysis to only largest circles, we find that circles reflect not only node-level attributes but also of topological importance. These findings clarify the distinction between local attribute-driven circles and global community structures, thus highlighting the strategic importanc of overlapping nodes in spreading dynamics. This provides foundation for future research on overlapping nodes in both circles and communities.
Adaptive Knowledge Transferring with Switching Dual-Student Framework for Semi-Supervised Medical Image Segmentation
Venue: arXiv cs.CV 2026
Year: 2026

Teacher-student frameworks have emerged as a leading approach in semi-supervised medical image segmentation, demonstrating strong performance across various tasks. However, the learning effects are still limited by the strong correlation and unreliable knowledge transfer process between teacher and student networks. To overcome this limitation, we introduce a novel switching Dual-Student architecture that strategically selects the most reliable student at each iteration to enhance dual-student collaboration and prevent error reinforcement. We also introduce a strategy of Loss-Aware Exponential Moving Average to dynamically ensure that the teacher absorbs meaningful information from students, improving the quality of pseudo-labels. Our plug-and-play framework is extensively evaluated on 3D medical image segmentation datasets, where it outperforms state-of-the-art semi-supervised methods, demonstrating its effectiveness in improving segmentation accuracy under limited supervision.
CodeWiki: Evaluating AI's Ability to Generate Holistic Documentation for Large-Scale Codebases
Venue: arXiv cs.SE 2026
Year: 2026

Given a large and evolving codebase, the ability to automatically generate holistic, architecture-aware documentation that captures not only individual functions but also cross-file, cross-module, and system-level interactions remains an open challenge. Comprehensive documentation is essential for long-term software maintenance and collaboration, yet current automated approaches still fail to model the rich semantic dependencies and architectural structures that define real-world software systems. We present \textbf{CodeWiki}, a unified framework for automated repository-level documentation across seven programming languages. CodeWiki introduces three key innovations: (i) hierarchical decomposition that preserves architectural context across multiple levels of granularity, (ii) recursive multi-agent processing with dynamic task delegation for scalable generation, and (iii) multi-modal synthesis that integrates textual descriptions with visual artifacts such as architecture diagrams and data-flow representations. To enable rigorous evaluation, we introduce \textbf{CodeWikiBench}, a comprehensive benchmark featuring multi-dimensional rubrics and LLM-based assessment protocols. Experimental results show that CodeWiki achieves a 68.79\% quality score with proprietary models, outperforming the closed-source DeepWiki baseline (64.06\%) by 4.73\%, with particularly strong improvements on high-level scripting languages (+10.47\%). We open-source CodeWiki to foster future research and community adoption.
Open Korean Historical Corpus: A Millennia-Scale Diachronic Collection of Public Domain Texts
Venue: arXiv cs.CL 2026
Year: 2026

The history of the Korean language is characterized by a discrepancy between its spoken and written forms and a pivotal shift from Chinese characters to the Hangul alphabet. However, this linguistic evolution has remained largely unexplored in NLP due to a lack of accessible historical corpora. To address this gap, we introduce the Open Korean Historical Corpus, a large-scale, openly licensed dataset spanning 1,300 years and 6 languages, as well as under-represented writing systems like Korean-style Sinitic (Idu) and Hanja-Hangul mixed script. This corpus contains 17.7 million documents and 5.1 billion tokens from 19 sources, ranging from the 7th century to 2025. We leverage this resource to quantitatively analyze major linguistic shifts: (1) Idu usage peaked in the 1860s before declining sharply; (2) the transition from Hanja to Hangul was a rapid transformation starting around 1890; and (3) North Korea's lexical divergence causes modern tokenizers to produce up to 51 times higher out-of-vocabulary rates. This work provides a foundational resource for quantitative diachronic analysis by capturing the history of the Korean language. Moreover, it can serve as a pre-training corpus for large language models, potentially improving their understanding of Sino-Korean vocabulary in modern Hangul as well as archaic writing systems.
BEST-RQ-Based Self-Supervised Learning for Whisper Domain Adaptation
Venue: arXiv cs.CL 2026
Year: 2026

Automatic Speech Recognition (ASR) systems, despite large multilingual training, struggle in low-resource scenarios where labeled data is scarce. We propose BEARD (BEST-RQ Encoder Adaptation with Re-training and Distillation), a novel framework designed to adapt Whisper's encoder with unlabeled data. Unlike traditional self-supervised learning methods, BEARD uniquely combines a BEST-RQ objective with knowledge distillation from a frozen teacher encoder, ensuring the encoder's complementarity with the pre-trained decoder. Our experiments focus on the ATCO2 corpus from the challenging Air Traffic Control (ATC) communications domain, characterized by non-native speech, noise, and specialized phraseology. Using about 5,000 hours of untranscribed speech for BEARD and 2 hours of transcribed speech for fine-tuning, the proposed approach significantly outperforms previous baseline and fine-tuned model, achieving a relative improvement of 12% compared to the fine-tuned model. To the best of our knowledge, this is the first work to use a self-supervised learning objective for domain adaptation of Whisper.
Semi-supervised and unsupervised learning for health indicator extraction from guided waves in aerospace composite structures
Venue: arXiv cs.LG 2026
Year: 2026

Health indicators (HIs) are central to diagnosing and prognosing the condition of aerospace composite structures, enabling efficient maintenance and operational safety. However, extracting reliable HIs remains challenging due to variability in material properties, stochastic damage evolution, and diverse damage modes. Manufacturing defects (e.g., disbonds) and in-service incidents (e.g., bird strikes) further complicate this process. This study presents a comprehensive data-driven framework that learns HIs via two learning approaches integrated with multi-domain signal processing. Because ground-truth HIs are unavailable, a semi-supervised and an unsupervised approach are proposed: (i) a diversity deep semi-supervised anomaly detection (Diversity-DeepSAD) approach augmented with continuous auxiliary labels used as hypothetical damage proxies, which overcomes the limitation of prior binary labels that only distinguish healthy and failed states while neglecting intermediate degradation, and (ii) a degradation-trend-constrained variational autoencoder (DTC-VAE), in which the monotonicity criterion is embedded via an explicit trend constraint. Guided waves with multiple excitation frequencies are used to monitor single-stiffener composite structures under fatigue loading. Time, frequency, and time-frequency representations are explored, and per-frequency HIs are fused via unsupervised ensemble learning to mitigate frequency dependence and reduce variance. Using fast Fourier transform features, the augmented Diversity-DeepSAD model achieved 81.6% performance, while DTC-VAE delivered the most consistent HIs with 92.3% performance, outperforming existing baselines.
Evolving Interactive Diagnostic Agents in a Virtual Clinical Environment
Venue: arXiv cs.CL 2026
Year: 2026

We present a framework for training large language models (LLMs) as diagnostic agents with reinforcement learning, enabling them to manage multi-turn interactive diagnostic processes, adaptively select examinations, and commit to final diagnoses. Unlike instruction-tuned models trained on static data, our method acquires diagnostic strategies through dynamic exploration and outcome-based feedback, mapping evolving patient states to the next optimal examination and subsequent diagnosis. Our contributions include: (i) DiagGym, a diagnostics world model trained with electronic health records, serving as a virtual clinical environment to support closed-loop in-silico training and evaluation for interactive diagnosis; (ii) DiagAgent, trained via end-to-end multi-turn RL to learn dynamic diagnostic policies that optimize both interactive effectiveness and final accuracy; (iii) DiagBench, a multi-center diagnostic benchmark designed to evaluate multi-turn diagnostic interaction trajectories. The benchmark comprises 2.2K physician-validated cases sourced from 4 distinct distributions, alongside 3.3K physician-written rubrics for granular process-oriented evaluation. (iv) Extensive evaluations demonstrate DiagAgent's superior performance across both in-domain and out-of-domain (OOD) settings. DiagAgent significantly outperforms 11 SOTA LLMs and 2 prompt-engineered agents. In the end-to-end setting, it delivers a 11.20% increase in diagnostic accuracy and a 17.58% boost in examination recommendation F1 score, while consistently maintaining SOTA performance across all three external centers. Furthermore, in rubric-based evaluations, it surpasses the next-best model by 7.1% in weighted rubric score. These findings indicate that learning policies in interactive clinical environments confers long-term diagnostic management abilities unattainable through passive training.
SwiftEmbed: Ultra-Fast Text Embeddings via Static Token Lookup for Real-Time Applications
Venue: arXiv cs.CL 2026
Year: 2026

We present SwiftEmbed, a production-oriented serving system for static token embeddings that achieves 1.12\,ms p50 latency for single-text requests while maintaining a 60.6 MTEB average score across 8 representative tasks. Built around the open-source Potion-base-8M distilled model from MinishLab and implemented in Rust, the system delivers 50,000 requests per second through static embedding lookup, mean pooling, and zero-copy IEEE754 binary serialization. Evaluation demonstrates exceptional duplicate detection performance (90.1% AP) and strong semantic similarity (76.1% Spearman correlation). Performance relative to Sentence-BERT is task-dependent: robust for deduplication and similarity workloads (89--100%), substantially lower for classification and complex retrieval tasks (75%). Domain-specific performance ranges from 75% to 131% of a GloVe-840B baseline. The system targets real-time embedding applications where sub-5\,ms latency is operationally critical and where full transformer inference is not feasible.
SemCoT: Accelerating Chain-of-Thought Reasoning through Semantically-Aligned Implicit Tokens
Venue: arXiv cs.CL 2026
Year: 2026

The verbosity of Chain-of-Thought (CoT) reasoning hinders its mass deployment in efficiency-critical applications. Recently, implicit CoT approaches have emerged, which encode reasoning steps within LLM's hidden embeddings (termed ``implicit reasoning'') rather than explicit tokens. This approach accelerates CoT by reducing the reasoning length and bypassing some LLM components. However, existing implicit CoT methods face two significant challenges: (1) they fail to preserve the semantic alignment between the implicit reasoning (when transformed to natural language) and the ground-truth reasoning, resulting in a significant CoT performance degradation, and (2) they focus on reducing the length of the implicit reasoning; however, they neglect the considerable time cost for an LLM to generate one individual implicit reasoning token. To tackle these challenges, we propose a novel semantically-aligned implicit CoT framework termed SemCoT. In particular, for the first challenge, we design a contrastively trained sentence transformer that evaluates semantic alignment between implicit and explicit reasoning, which is used to enforce semantic preservation during implicit reasoning optimization. To address the second challenge, we introduce an efficient implicit reasoning generator by finetuning a lightweight language model using knowledge distillation. This generator is guided by our sentence transformer to distill ground-truth reasoning into semantically aligned implicit reasoning, while also optimizing for accuracy. SemCoT is the first approach that enhances CoT efficiency by jointly optimizing token-level generation speed and preserving semantic alignment with ground-truth reasoning. Extensive experiments demonstrate the superior performance of SemCoT compared to state-of-the-art methods in both efficiency and effectiveness. Our code can be found at https://github.com/YinhanHe123/SemCoT/.
Cyclic Counterfactuals under Shift-Scale Interventions
Venue: arXiv cs.AI 2026
Year: 2026

Most counterfactual inference frameworks traditionally assume acyclic structural causal models (SCMs), i.e. directed acyclic graphs (DAGs). However, many real-world systems (e.g. biological systems) contain feedback loops or cyclic dependencies that violate acyclicity. In this work, we study counterfactual inference in cyclic SCMs under shift-scale interventions, i.e., soft, policy-style changes that rescale and/or shift a variable's mechanism.
Most Juntas Saturate the Hardcore Lemma
Venue: arXiv cs.CC 2026
Year: 2026

Consider a function that is mildly hard for size-$s$ circuits. For sufficiently large $s$, Impagliazzo's hardcore lemma guarantees a constant-density subset of inputs on which the same function is extremely hard for circuits of size $s'<\!\!<s$. Blanc, Hayderi, Koch, and Tan [FOCS 2024] recently showed that the degradation from $s$ to $s'$ in this lemma is quantitatively tight in certain parameter regimes. We give a simpler and more general proof of this result in almost all parameter regimes of interest by showing that a random junta witnesses the tightness of the hardcore lemma with high probability.
From Medical Records to Diagnostic Dialogues: A Clinical-Grounded Approach and Dataset for Psychiatric Comorbidity
Venue: arXiv cs.AI 2026
Year: 2026

Psychiatric comorbidity is clinically significant yet challenging due to the complexity of multiple co-occurring disorders. To address this, we develop a novel approach integrating synthetic patient electronic medical record (EMR) construction and multi-agent diagnostic dialogue generation. We create 502 synthetic EMRs for common comorbid conditions using a pipeline that ensures clinical relevance and diversity. Our multi-agent framework transfers the clinical interview protocol into a hierarchical state machine and context tree, supporting over 130 diagnostic states while maintaining clinical standards. Through this rigorous process, we construct PsyCoTalk, the first large-scale dialogue dataset supporting comorbidity, containing 3,000 multi-turn diagnostic dialogues validated by psychiatrists. This dataset enhances diagnostic accuracy and treatment planning, offering a valuable resource for psychiatric comorbidity research. Compared to real-world clinical transcripts, PsyCoTalk exhibits high structural and linguistic fidelity in terms of dialogue length, token distribution, and diagnostic reasoning strategies. Licensed psychiatrists confirm the realism and diagnostic validity of the dialogues. This dataset enables the development and evaluation of models capable of multi-disorder psychiatric screening in a single conversational pass.
SynHLMA:Synthesizing Hand Language Manipulation for Articulated Object with Discrete Human Object Interaction Representation
Venue: arXiv cs.RO 2026
Year: 2026

Generating hand grasps with language instructions is a widely studied topic that benefits from embodied AI and VR/AR applications. While transferring into hand articulatied object interaction (HAOI), the hand grasps synthesis requires not only object functionality but also long-term manipulation sequence along the object deformation. This paper proposes a novel HAOI sequence generation framework SynHLMA, to synthesize hand language manipulation for articulated objects. Given a complete point cloud of an articulated object, we utilize a discrete HAOI representation to model each hand object interaction frame. Along with the natural language embeddings, the representations are trained by an HAOI manipulation language model to align the grasping process with its language description in a shared representation space. A joint-aware loss is employed to ensure hand grasps follow the dynamic variations of articulated object joints. In this way, our SynHLMA achieves three typical hand manipulation tasks for articulated objects of HAOI generation, HAOI prediction and HAOI interpolation. We evaluate SynHLMA on our built HAOI-lang dataset and experimental results demonstrate the superior hand grasp sequence generation performance comparing with state-of-the-art. We also show a robotics grasp application that enables dexterous grasps execution from imitation learning using the manipulation sequence provided by our SynHLMA. Our codes and datasets will be made publicly available.